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Tag: Index

RNAsifter 1.0

:: DESCRIPTION

RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.

MuGI 1.0

:: DESCRIPTION

MuGI is a compressed index of collections of genomes of the same species. It allows to ask for both exact and approximate queries. The input data must be given as a reference sequence and Variant Call Format (VCF) file describing the differences between individual genomes and reference genome.

Gk-arrays 2.1.0

:: DESCRIPTION

Gk-arrays are provided as a simple-to-use C++ library dedicated to queries on large collection of sequences as produced by high-throughput sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).Gk-arrays index k-mers of reads and allow to answer different queries on that read collection.

GEM library PR3

:: DESCRIPTION

GEM Library (GEnome Multi-tool) is a set of very optimized tools for indexing/querying huge genomes/files. Provided so far are a very fast exhaustive mapper (the GEM mapper), an unconstrained split mapper (the GEM split mapper), and a very fast program to compute genome mappability (the GEM mappability).

HS

:: DESCRIPTION

HS (host specificity) provided here calculates an index of host specificity for parasites based on the number of species, genera, families, orders, and classes in which a species is found. It incorporates the hierarchical information about host distribution included in the Linnean hierarchy, but it is not explcitly tree based.